Bio::Taxonomy::Taxon(3pm) User Contributed Perl Documentation Bio::Taxonomy::Taxon(3pm)
NAME
Bio::Taxonomy::Taxon - Generic Taxonomic Entity object
SYNOPSIS
# NB: This module is deprecated. Use Bio::Taxon instead.
use Bio::Taxonomy::Taxon;
my $taxonA = Bio::Taxonomy::Taxon->new();
my $taxonL = Bio::Taxonomy::Taxon->new();
my $taxonR = Bio::Taxonomy::Taxon->new();
my $taxon = Bio::Taxonomy::Taxon->new();
$taxon->add_Descendents($taxonL);
$taxon->add_Descendents($taxonR);
my $species = $taxon->species;
DESCRIPTION
Makes a taxonomic unit suitable for use in a taxonomic tree
AUTHOR
Dan Kortschak email kortschak@rsbs.anu.edu.au
CONTRIBUTORS
Sendu Bala: bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Taxonomy::Taxon->new();
Function: Builds a new Bio::Taxonomy::Taxon object
Returns : Bio::Taxonomy::Taxon
Args : -descendents => array pointer to descendents (optional)
-branch_length => branch length [integer] (optional)
-taxon => taxon
-id => unique taxon id for node (from NCBI's list preferably)
-rank => the taxonomic level of the node (also from NCBI)
add_Descendent
Title : add_Descendent
Usage : $taxon->add_Descendent($taxon);
Function: Adds a descendent to a taxon
Returns : number of current descendents for this taxon
Args : Bio::Taxonomy::Taxon
boolean flag, true if you want to ignore the fact that you are
adding a second node with the same unique id (typically memory
location reference in this implementation). default is false and
will throw an error if you try and overwrite an existing node.
each_Descendent
Title : each_Descendent($sortby)
Usage : my @taxa = $taxon->each_Descendent;
Function: all the descendents for this taxon (but not their descendents
i.e. not a recursive fetchall)
Returns : Array of Bio::Taxonomy::Taxon objects
Args : $sortby [optional] "height", "creation" or coderef to be used
to sort the order of children taxa.
remove_Descendent
Title : remove_Descendent
Usage : $taxon->remove_Descedent($taxon_foo);
Function: Removes a specific taxon from being a Descendent of this taxon
Returns : nothing
Args : An array of Bio::taxonomy::Taxon objects which have be previously
passed to the add_Descendent call of this object.
remove_all_Descendents
Title : remove_all_Descendents
Usage : $taxon->remove_All_Descendents()
Function: Cleanup the taxon's reference to descendents and reset
their ancestor pointers to undef, if you don't have a reference
to these objects after this call they will be cleanedup - so
a get_nodes from the Tree object would be a safe thing to do first
Returns : nothing
Args : none
get_Descendents
Title : get_Descendents
Usage : my @taxa = $taxon->get_Descendents;
Function: Recursively fetch all the taxa and their descendents
*NOTE* This is different from each_Descendent
Returns : Array or Bio::Taxonomy::Taxon objects
Args : none
ancestor
Title : ancestor
Usage : $taxon->ancestor($newval)
Function: Set the Ancestor
Returns : value of ancestor
Args : newvalue (optional)
branch_length
Title : branch_length
Usage : $obj->branch_length($newval)
Function:
Example :
Returns : value of branch_length
Args : newvalue (optional)
description
Title : description
Usage : $obj->description($newval)
Function:
Returns : value of description
Args : newvalue (optional)
rank
Title : rank
Usage : $obj->rank($newval)
Function: Set the taxonomic rank
Returns : taxonomic rank of taxon
Args : newvalue (optional)
taxon
Title : taxon
Usage : $obj->taxon($newtaxon)
Function: Set the name of the taxon
Example :
Returns : name of taxon
Args : newtaxon (optional)
id
Title : id
Usage : $obj->id($newval)
Function:
Example :
Returns : value of id
Args : newvalue (optional)
internal_id
Title : internal_id
Usage : my $internalid = $taxon->internal_id
Function: Returns the internal unique id for this taxon
(a monotonically increasing number for this in-memory implementation
but could be a database determined unique id in other
implementations)
Returns : unique id
Args : none
_creation_id
Title : _creation_id
Usage : $obj->_creation_id($newval)
Function: a private method signifying the internal creation order
Returns : value of _creation_id
Args : newvalue (optional)
is_Leaf
Title : is_Leaf
Usage : if( $node->is_Leaf )
Function: Get Leaf status
Returns : boolean
Args : none
to_string
Title : to_string
Usage : my $str = $taxon->to_string()
Function: For debugging, provide a taxon as a string
Returns : string
Args : none
height
Title : height
Usage : my $len = $taxon->height
Function: Returns the height of the tree starting at this
taxon. Height is the maximum branchlength.
Returns : The longest length (weighting branches with branch_length) to a leaf
Args : none
invalidate_height
Title : invalidate_height
Usage : private helper method
Function: Invalidate our cached value of the taxon's height in the tree
Returns : nothing
Args : none
classify
Title : classify
Usage : @obj->classify()
Function: a method to return the classification of a species
Returns : name of taxon and ancestor's taxon recursively
Args : boolean to specify whether we want all taxa not just ranked
levels
has_rank
Title : has_rank
Usage : $obj->has_rank($rank)
Function: a method to query ancestors' rank
Returns : boolean
Args : $rank
has_taxon
Title : has_taxon
Usage : $obj->has_taxon($taxon)
Function: a method to query ancestors' taxa
Returns : boolean
Args : Bio::Taxonomy::Taxon object
distance_to_root
Title : distance_to_root
Usage : $obj->distance_to_root
Function: a method to query ancestors' taxa
Returns : number of links to root
Args :
recent_common_ancestor
Title : recent_common_ancestor
Usage : $obj->recent_common_ancestor($taxon)
Function: a method to query find common ancestors
Returns : Bio::Taxonomy::Taxon of query or undef if no ancestor of rank
Args : Bio::Taxonomy::Taxon
species
Title : species
Usage : $obj=$taxon->species;
Function: Returns a Bio::Species object reflecting the taxon's tree position
Returns : a Bio::Species object
Args : none
perl v5.14.2 2012-03-02 Bio::Taxonomy::Taxon(3pm)